Docking study of cistanoside C to telomeric DNA fragment

Experiments show that the natural products phenyl propanoid glycosides (PPGs) extracted from the plant Pedicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecule Cistanoside C and telomeric DNA fragment has been carried out. The docking calculations performed using JUMNA software showed that the Cistanoside C could be docked into the minor groove of telomeric DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the saccharide side-groups.     

Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking

Experiments show that the natural substances phenylpropanoid glycosides (PPGs) extracted from pelicularis spicata are capable of repairing DNA damaged by oxygen radicals. Based on kinetic measurements and experiments on tumor cells, a theoretical study of the interaction between PPG molecules and isolated DNA bases, as well as a DNA fragment has been performed. An interaction mechanism reported early has been refined. The docking calculations performed using junction minimization of nucleic acids (JUMNA) software showed that the PPG molecules can be docked into the minor groove of DNA and form complexes with the geometry suitable for an electron transfer between guanine radical and the ligand. Such complexes can be formed without major distortions of DNA structure and are further stabilized by the interaction with the rhamnosyl side-groups.     

C36衍生物C36H12和C36X12簇分子的理论研究

采用从虎ＨＦ／ＳＴＯ－３Ｇ方法,对３６及其衍生物Ｃ３６Ｈ１２和Ｃ３６Ｘ１２（Ｘ＝Ｆ,Ｃｌ,Ｂｒ,Ｉ）进行计算研究,讨论了Ｃ３６Ｈ１２和Ｃ３６Ｘ１２簇分子几何结构随卤素Ｘ原子序数变化的规律,分子的稳定性及电荷转移情况,结果表明,Ｃ３６Ｈ１２和Ｃ３６Ｆ１２在所有簇分子中是较为稳定的。     

Theoretical study of structure and stability of fullerene derivative: C50O

A total of eight possible isomers of C₅₀O, an oxide of fullerene C₅₀ (D_5h), have been investigated by B3LYP/3‐21G calculations. The isomer, which has an annulene‐like structure with oxygen bridging across a [5,6] type C? C bond at the site between the pole and the equatorial belt, is found being the ground state of C₅₀O. Four isomers are relatively more stable and the energy differences between them are not large. This result indicates that more than one C₅₀O isomer will coexist once C₅₀O is synthesized. The relative stabilities of the C₅₀O isomers may be determined mainly by the strain release and by the formation of the cyclic phenylene substructure at the equatorial belt of the cage. The calculated nucleus independent chemical shifts (NICS) of the C₅₀O isomers will be useful because from them one can expect outstanding NMR properties that can lead to their identification and characterization. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of fullerene derivatives: C40H4 and C40X4 cluster molecules

Herein we demonstrate that the C₄₀ cluster molecule is easily formed to T_d symmetry structure and its ground state is ⁵A₂ open shell with four unpaired electrons. These four unpaired electrons are located at the tip points of the T_d symmetry structure. This work also indicates that these four unpaired electrons can easily react with a single valence atom, such as hydrogen or halogen atoms, to form a stable carbon hydrogen cluster molecule, C₄₀H₄, and carbon halogen cluster molecules, C₄₀X₄ (X=F, Cl, Br, I), respectively. The PM3 semiempirical molecular orbital method from Gaussian 94W computer program package was applied very well to these cluster molecules. According to the results in this study, the structures of geometrical optimization, ionization potential, energy gap, heat of formation, atomization energy, vibration frequency, and the remaining data of C₄₀H₄ and C₄₀X₄ cluster molecules. The above-calculated data prove that these unknown cluster molecules are stable and have a stable capacity similar to 1,3,5,7-tetrahaloadamantane molecules. They can be possibly synthesized experimentally in the near future. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 273–284, 1998     

Theoretical study of fullerene derivatives: C28H4 and C28X4 cluster molecules

Based on the basic theory of C₂₈ cluster molecule proven by H. W. Kroto and the research findings of C₂₈'s derivative such as Ti@C₂₈* and Mg@C₂₈, proven by T. Guo, B. I. Dunlap, O. D. Haberlen, and others, we examine the two series fullerene derivatives, C₂₈H₄ and C₂₈X₄ cluster molecules, which are formed by the skeleton of C₂₈ cluster molecule. In this work, we not only prove that C₂₈ cluster molecule belongs to the T_d symmetry structure and its ground state is ⁵A₂ open-shell with four unpaired electrons, but also find that C₂₈ can easily react with single valence electron atoms, like hydrogen atom and halogen atoms, to be formed to stable fullerene derivatives, C₂₈H₄ and C₂₈X₄ cluster molecules (X=F, Cl, Br, I). The PM3 semiempirical molecular orbital method from G94W and Hyperchem program packages were applied very well in these fullerene derivatives. According to the results presented herein, we obtain the structures of geometrical optimization, ionization potential energy gap, heat of formation, atomization energy, and vibration frequency data of the C₂₈H₄ and C₂₈X₄ cluster molecules. The above calculation data confirm that these unknown fullerene derivatives are stable molecules; the stable behavior resembles the 1,3,5,7-tetrahaloadamantane molecules. It is quite possible that they can be synthesized experimentally in the near future. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 187–197, 1998     

ChemInform Abstract: Theoretical Study of C90 and C96 Fullerene Isomers.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.     

Theoretical and Experimental Investigation of the Antioxidation Mechanism of Loureirin C by Radical Scavenging for Treatment of Stroke

Recent pharmacological studies have shown that dragon’s blood has an anti-cerebral ischemia effect. Loureirin C (LC), a kind of dihydrochalcone compound in dragon’s blood, is believed to be play an important role in the treatment of ischemia stroke, but fewer studies for LC have been done. In this paper, we report the first experimental and theoretical studies on the antioxidation mechanism of LC by radical scavenging. The experimental studies show that LC has almost no effect on cell viability under 15 μM for the SH-SY5Y cells without any treatments. For the SH-SY5Y cells with oxygen and glucose deprivation-reperfusion (OGD/R) treatment, LC increased the viability of SH-SY5Y cells. The results of 2′,7′-Dichlorodihydrofluorescein diacetate (DCFH-DA) and MitoSox Red experiments indicate that LC is very efficient in inhibiting the generation of the intracellular/mitochondrial reactive oxygen species (ROS) or removing these two kinds of generated ROS. The density functional theory (DFT) calculations allowed us to elucidate the antioxidation mechanisms of LC. Fukui function analysis reveals the radical scavenging of LC by hydrogen abstraction mechanism, the complex formation by e-transfer, and radical adduct formation (RAF) mechanism. Among the H-abstraction, the complex formation by e-transfer, and radical adduct formation (RAF) reactions on LC, the H-abstraction at O-H35 position by OH^• is favorable with the smallest energy difference between the product and two reactants of the attack of OH^• to LC of −0.0748 Ha. The bond dissociation enthalpies (BDE), proton affinities (PA), ionization potential (IP), proton dissociation enthalpy (PDE), and electron transfer enthalpy (ETE) were calculated to determine thermodynamically preferred reaction pathway for hydrogen abstraction mechanism. In water, IP and the lowest PDE value at O3-H35 position are lower than the lowest BDE value at O3-H35 position; 41.8986 and 34.221 kcal/mol, respectively, indicating that SEPT mechanism is a preferred one in water in comparison with the HAT mechanism. The PA value of O3-H35 of LC in water is −17.8594 kcal/mol, thus the first step of SPLET would occur spontaneously. The minimum value of ETE is higher than the minimum value of PDE at O3-H35 position and IP value, 14.7332 and 22.4108 kcal/mol, respectively, which suggests that the SEPT mechanism is a preferred one in water in comparison with the SPLET mechanism. Thus, we can draw a conclusion that the SEPT mechanism of is the most favorite hydrogen abstraction mechanism in water, and O-H35 hydroxyl group has the greatest ability to donate H-atoms.     

Theoretical and kinetic study of the H + C2H5CN reaction

The reaction of H radical with C₂H₅CN has been studied using various quantum chemistry methods. The geometries were optimized at the B3LYP/6‐311+G(d,p) and B3LYP/6‐311++G(2d,2p) levels. The single‐point energies were calculated using G3 and BMC‐CCSD methods based on B3LYP/6‐311++G(2d,2p) geometries. Four mechanisms were investigated, namely, hydrogen abstraction, C‐addition/elimination, N‐addition/elimination and substitution. The kinetics of this reaction were studied using the transition state theory and multichannel Rice‐Ramsperger‐Kassel‐Marcus methodologies over a wide temperature range of 200–3000 K. The calculated results indicate that C‐addition/elimination channel is the most feasible over the whole temperature range. The deactivation of initial adduct C₂H₅CHN is dominant at lower temperature with bath gas H₂ of 760 Torr; whereas C₂H₅+HCN is the dominant product at higher temperature. Our calculated rate constants are in good agreement with the available experimental data. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical study on the structures and electronic spectra of C120On (n=1,2)

ZINDO series calculations have been carried out to study the double‐cage oxides C₁₂₀O_n (n=1,2). The results show that the formation of a furan ring by the bridge‐bond between the two cages connected the two C₆₀ fullerene units and formed the C₁₂₀O with C_2v symmetry. C₁₂₀O₂ has two isomers with C_2v symmetry depending on either 6–6 or 6–5 connection between the two cages. Two furan rings and a pure four‐member ring form in this molecule. The formation of C₁₂₀O assuages the constraint of epoxide structure in C₆₀O, shortens the distance of the monomers, and produces some finite interaction between the two balls. More bonding in C₁₂₀O₂ shortens the distance of the two cages further and brings about stronger interaction. However, the two cages in C₁₂₀O_n (n=1,2) behave somehow independently that the electronic spectra of C₁₂₀O_n (n=1,2) are similar to those of C₆₀. The 6–6 connection isomer of C₁₂₀O₂ is more stable; its spectra are in good agreement with those of the experiment. The calculated electronic spectra of C₁₂₀O not only are in good agreement with the experiment in the ultraviolet region but also get some weak peaks in the visible region (>400 nm) not observed in experiment. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 291–307, 2000     

Theoretical study on structures and stabilities of [H,Ge,C,N

Theoretical investigations are performed for the first time on the simplest hydrogenated germanium cyanide [H,Ge,C,N], whose analogs [H,C(2),N] and [H,Si,C,N] have been detected in space and laboratory, respectively. The detailed potential energy surfaces in both singlet and triplet states are constructed at the CCSD(T)/6-311+G(3df,2p)//B3LYP/6-31G(d)+ZPVE level, including 18 minimum isomers and 26 interconversion transition states. The former three low-lying and kinetically stabilized isomers are HGeCN (1)1 (0.0 kcal/mol), HGeNC (1)2 (5.1 kcal/mol), and cyclic cCHNGe(1)7 (11.1 kcal/mol). In addition, five isomers HCNGe (1)3 (33.8), HNCGe (1)5 (29.8), cNHCGe (1)8 (37.9), HGeCN (3)1 (30.1), and HNCGe (3)5 (26.5) each have considerable barriers, despite their high energies. Future laboratory characterization and astrophysical detection of the eight [H,Ge,C,N] isomers, especially the former three low-lying species (1)1, (1)2, and (1)7, are highly recommended. The accurate spectroscopic data at the QCISD/6-311G(d,p) level are provided. For some species, the CBS-QB3 calculations are also performed. Wherever possible, comparisons with the analogous [H,C(2),N] and [H,Si,C,N] are made on the structural, energetic, and bonding properties.     

Damage to DNA in bacterioplankton: a model of damage by ultraviolet radiation and its repair as influenced by vertical mixing

A model of UV-induced DNA damage in oceanic bacterioplankton was developed and tested against previously published and novel measurements of cyclobutane pyrimidine dimers (CPD) in surface layers of the ocean. The model describes the effects of solar irradiance, wind-forced mixing of bacterioplankton and optical properties of the water on net DNA damage in the water column. The biological part includes the induction of CPD by UV radiation and repair of this damage through photoreactivation and excision. The modeled damage is compared with measured variability of CPD in the ocean: diel variation in natural bacterioplankton communities at the surface and in vertical profiles under different wind conditions (net damage as influenced by repair and mixing); in situ incubation of natural assemblages of bacterioplankton (damage and repair, no mixing); and in situ incubation of DNA solutions (no repair, no mixing). The model predictions are generally consistent with the measurements, showing similar patterns with depth, time and wind speed. A sensitivity analysis assesses the effect on net DNA damage of varying ozone thickness, colored dissolved organic matter concentration, chlorophyll concentration, wind speed and mixed layer depth. Ozone thickness and mixed layer depth are the most important factors affecting net DNA damage in the mixed layer. From the model, the total amplification factor (TAF; a relative measure of the increase of damage associated with a decrease in ozone thickness) for net DNA damage in the euphotic zone is 1.7, as compared with 2.1-2.2 for irradiance weighted for damage to DNA at the surface.     

Theoretical studies of structures and stabilities of a new odd-numbered fullerene dimer: C141

The possible isomers of a newly synthesized C(141) molecule are calculated using MNDO, AM1, PM3, B3LYP/3-21G, and B3LYP/6-31G(d) methods. The geometry optimizations showed that the isomer 8-8 has the lowest total energy in all 64 possible structures of C(141). Unlike those of C(130), C(140), etc., the C(141) 8-8 shows a new structure: two C(70) side cages open [6.6] ring junctions located at the equator (instead of cap) area to create new chemical bonds for the bridge atom. Theoretical measurements of the average length of the long and short axes of C(70) side cages in the C(141) molecule reveal that when two C(70) cages are connected with each other at the equators, their geometric shapes become more spherical compared with the pristine C(70); this leads to a reduction of the molecular polarizability. Analysis of the local and global strain indicates that the global strain of C(70) monomer in the C(141) 8-8 is greatly reduced compared to the pristine C(70). The stable C(70) derivatives that are formed with reacted C-C bonds in the equator area may put new insights into fullerene chemistry, in particular, for C(70) to react with a large molecule. The results are discussed together with the experimental data.     

Possible DNA damage by oxidation products of guanine: A density functional and electron propagator theoretical study

The stability and reactivity of seven guanine oxidation products (GOP), which contain 8‐oxo‐7,8‐dihydroguanine (8‐oxoG) have been studied and compared with the four nucleobases, such as adenine, cytosine, guanine, and thymine. It has been possible with the use of density functional theory and electron propagator theory (EPT), to evaluate their relation with certain ionization induced process, which produce damage to DNA. Using the application of Koopmans's theorem, EPT provides alternatively a reliable way to calculate the vertical ionization potential (VIP) and vertical electron affinity (VEA). This process has been used to obtain other reactivity indexes, such as: electronegativity and hardness. In the nucleobases and the GOP studies, we observed the following: guanine and 8‐oxo‐7,8‐dihydroguanine were the lowest VIP, and 8‐oxoG was the lowest hardness. This let us confirm that these species are the most susceptible to change their electron densities and transform in other GOP. Particularly, the GOP, Sp(R), Sp(S), and Z were the highest VIP. It allows us to say that they are the most stable. Z and Iz were the highest VEA; this suggests that they have a big capacity to accept electrons and form anionic centers in DNA. The GOP, which was considered in this study, showed hardness values between 9.1 and 10.4 because of π‐conjugation; therefore, these GOP could be good candidates to participate in DNA transversions. © 2012 Wiley Periodicals, Inc.     

Theoretical study on the structures and electron spectra of C60M12 (M=Li,Na, Be)

Intermediate neglect of differential overlap (INDO) method was used to study the structures and the electronic spectra of C₆₀M₁₂ (M=Li, Na, Be). The calculations indicate that in the minimal energy configuration of C₆₀M₁₂ (M=Li, Na) the C₆₀ cage still retains I_h symmetry and the 12 Li or Na atoms are symmetrically located above the pentagons of the C₆₀ cage, whereas the difference between the double and single bonds has been significantly reduced. In contrast, because six electrons are filled in the fivefold‐degenerated h_g orbital of C₆₀, the C_s structure of C₆₀Be₁₂ has illustrated the occurrence of Jahn‐Teller distortion. Based on the optimized geometries, the electronic absorption spectra were calculated and the nature of red shift was discussed. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 505–509, 1999     

Experimental and Theoretical Study of NiII- and PdII-Promoted Double Geminal C(sp3)−H Bond Activation Providing Facile Access to NHC Pincer Complexes: Isolated Intermediates and Mechanism

We report the first examples of metal-promoted double geminal activation of C(sp³)−H bonds of the N−CH₂−N moiety in an imidazole-type heterocycle, leading to nickel and palladium N-heterocyclic carbene complexes under mild conditions. Reaction of the new electron-rich diphosphine 1,3-bis((di-tert-butylphosphaneyl)methyl)-2,3-dihydro-1H-benzo[d]imidazole ( 1 ) with [PdCl₂(cod)] occurred in a stepwise fashion, first by single C−H bond activation yielding the alkyl pincer complex [PdCl(PC ^HP)] ( 3 ) with two trans phosphane donors and a covalent Pd−C bond. Activation of the C−H bond of the resulting α-methine C H−M group occurred subsequently when 3 was treated with HCl to yield the NHC pincer complex [PdCl(PC^NHCP)]Cl ( 2 ). Treatment of 1 with [NiBr₂(dme)] also afforded a NHC pincer complex, [NiBr(PC^NHCP)]Br ( 6 ), but the reactions leading to the double geminal C−H bond activation of the N−CH₂−N group were too fast to allow identification or isolation of an intermediate analogous to 3 . The determination of six crystal structures, the isolation of reaction intermediates and DFT calculations provided the basis for suggesting the mechanism of the stepwise transformation of a N−CH₂−N moiety in the N−C^NHC−N unit of NHC pincer complexes and explain the key differences observed between the Pd and Ni chemistries.     

Characterization of C12A7-O- Catalyst and Mechanism of Phenol Formation by Hydroxylation of Benzene

The benzene conversion and phenol selectivity from C6H6/O2/H2O over Ca24Al28O644+·4O-(C12A7-O-) catalyst were investigated using a flow reactor. The benzene conversion increases with the increase of temperature, and the phenol selectivity mainly depends on both reaction temperature and the composition of the mixtures. The changes of the catalyst structure before and after the reactions and the intermediates on the catalyst surface and in the bulk were investigated by XRD, EPR and FT-IR. The catalytic reactions do not cause any damage to the structure of the positively charged lattice framework C12A7-O-, but part of the O- and O2- species in the bulk of C12A7-O- translate to OH- after the reactions. The neutral species and anion intermediate were investigated by Q-MS and TOF-MS respectively. It is suggested that the active O- and OH- species played a key role in the process of phenol formation.     

Theoretical study of [Si,O,C,O] species: Prediction of new species on triplet potential energy surface

The intermediates [Si,O,C,O] of the Si + CO₂ reaction have been studied in detail using high level ab iniitio methods. Both singlet and triplet [Si,O,C,O] species are characterized structurally and energetically. On the singlet potential energy surface (PES), the vdw‐OSi–CO isomer and in the triplet PES, the bent‐SiOCO isomer is found to be thermodynamically as well as kinetically most stable species. All possible isomerization transition states (TS) are located on both singlet and triplet potential surfaces. On the triplet surface, the stability of the trans‐OSiCO isomer is comparable with that of the bent‐SiOCO isomer. A non‐planar cis‐SiOCO isomer is located on the triplet PES, which is predicted for the first time. Heats of formation at 0 K (Δ_fH°, 0 K) for all singlet and triplet species are computed using G3B3, G3MP2, and CBS‐Q theories. The discrepancy between G3B3 and the other two methods for the heat of formation value for triplet trans‐OSiCO is discussed. The PESs for singlet as well as triplet species with their dissociation asymptotes are explored at the CCSD(T)/6‐311G(d,p)//MP2/6‐311G(d,p) level of theory. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

ChemInform Abstract: Theoretical Studies of the Structure of Ti8Cl+ 12 Cluster: Existence of C12 Cage Structure Surrounded by Metal Atoms.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.